The intimate interplay between gut microbiota, host, and nutrient flow is crucial in defining the health status of the host. During microbial conventionalization of germfree mice, tightly regulated molecular responses assure the establishment of homeostasis and immune tolerance towards the microbiota. To decipher the temporal and regional dynamics of host-microbiota communication during the process of conventionalization, a combination of transcriptomics, (immune-)histology, metabonomics (tissue, urine, and plasma), as well as MITchip (Mouse Intestinal Tract chip) based microbiota profiling was employed. To this end, C57/B6 J germfree mice were conventionalized with mouse fecal microbiota and responses were followed in a time-resolved manner for thirty days. The colonizing microbiota was characterized by a shift from low towards higher diversity of its composition, over the period of conventionalization. Microbial colonization was rapidly (after one day) reflected by increased concentrations of specific urine and jejunal metabolites as well as by biologically relevant changes in jejunal tissue transcriptome profiles. Conversely, ileal and colonic transcriptome responses could be measured later, after four days post-conventionalization, and led towards stable molecular profiles at sixteen and thirty days of conventionalization, albeit with region-specific differences. The major molecular responses included strong induction of innate immune response followed by stimulation of adaptive and regulatory immune functions, as well as modulation of metabolic pathways involved in lipid, carbohydrate, and anabolic metabolism. Conventionalization was characterized by two stages separated by one stage of a single day which, particularly in the colon, resembled a transient stage of inflammation, based on transcriptomes, histology and transiently elevated levels of specific plasma markers. This state coincided with temporal domination of specific microbial groups that have previously been identified as “pathobionts”, suggestive of a transient state of dysbiosis. Extensive transcriptome profile analyses throughout the GI tract enabled the identification of central gene regulatory networks that govern the molecular responses during conventionalization and are proposed to serve as genetic signatures for the control of intestinal homeostasis in mice. Nearly all genes in these regulatory networks have human orthologues, suggesting that the biological findings of this study is also relevant for human intestinal biology. In support of this hypothesis, in the jejunum, the identified gene regulatory network appeared to be strongly associated with human metabolic disorders. This notion also suggests that at least in mice, possibly also in human, there is a prominent role of the proximal small intestine in systemic metabolic control.

This thesis exemplifies the pivotal role of the dynamic molecular interactions between the microbiota and the intestinal mucosa, in the establishment and maintenance of mucosal homeostasis in healthy mice. The molecular signatures obtained from these studies in mice may provide novel diagnostic tools and/or therapeutic targets in humans for specific disorders associated with intestinal dysbiosis and loss of mucosal homeostasis.